TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1954A/-:

update plot	correlation	link to info on gene
Rv1954c/-	(cc=0.6871)	info on Rv1954c/-
Rv2040c/-	(cc=0.5504)	info on Rv2040c/-
Rv2562/-	(cc=0.5253)	info on Rv2562/-
Rv3166c/-	(cc=0.5018)	info on Rv3166c/-
Rv1088/PE9	(cc=0.4774)	info on Rv1088/PE9
Rv1580c/-	(cc=0.4723)	info on Rv1580c/-
Rv1561/vapC11	(cc=0.4606)	info on Rv1561/vapC11
Rv1508A/-	(cc=0.4324)	info on Rv1508A/-
Rv1583c/-	(cc=0.4282)	info on Rv1583c/-
Rv2481c/-	(cc=0.4281)	info on Rv2481c/-

Correlation of Rv1954A/- with Rv1561/vapC11

Normalized LFCs for Rv1954A/-:
(description and provenance of datasets)

	Rv1954A/-	Rv1561/vapC11
Fe_supp_jason_reseq	-0.051	-0.437
low_pH_jason_reseq	-0.878	-0.097
NO_jason_reseq	0.795	-0.123
B6_jason_reseq	-1.023	-2.194
MHCII_jason_reseq	-0.98	-2.172
Isoniazid02	0.162	0.183
Rifampicin4	0.699	0.829
Ethambutol3	-0.047	3.934
Meropenem3	0.236	0.341
Vancomycin16	0.034	0.923
Rv2680_day32	0.267	0.775
H37Rv_KO_MarP	0.679	0.358
hypoxia_3wks	-0.909	0.303
hypoxia_6wks	-1.04	0.309
glycerol	-1.412	-0.592
cholesterol	-1.382	-0.847
AJ	-0.906	-0.101
Bibs02	-0.631	0.57
Bibs02c	-0.423	-0.444
BL6	1.662	1.315
BL6a	0.082	1.538
BXD01	-0.17	0.998
BXD010	0.235	1.712
BXD011	0.376	2.321
BXD03	1.021	2.179
BXD04	0.345	1.765
BXD05	1.009	2.034
BXD06	0.464	1.128
BXD07	0.734	1.8
BXD08	0.663	1.92
BXD09	0.683	2.109
CAST	-0.352	-0.612
CCcont	-0.105	1.704
DS01	-0.441	-0.38
DS02	-0.199	-1.115
DS04	0.049	-0.462
DS0c	-0.137	-0.699
GP01	-0.69	0.275
GP02	0.515	-0.871
GP0c	-0.193	0.425
NOD	-0.351	0.475
NZO	-1.113	0.202
PWK	-0.756	-0.22
H37Rv_KO_CtpC	-0.545	-0.145
H37Rv_KO_CtpD	-0.004	1.481
H37Rv_KO_Rv1272	1.449	0.059
H37Rv_KO_SugABC	-2.115	-0.022
H37Rv_KO_MbtN	-1.266	-0.565
Trans05	0.628	1.582
macrophage_unactivated	-0.174	0.085
IL1	-0.065	0.528
Rapamycin	0.7	0.424
Tcell	0.414	0.782
GMCSF	0.121	1.365
IFNab	0.78	0.263
IFNg	0.123	0.935
IFNg_GMCSF1	1.084	0.38
Rv1432_day32	0.746	-1.304
Rv1565c_day32	-0.839	-0.393
secA2_input	-1.506	0.235
delta_Rv3594	0.021	1.762
delta_Rv3717	0.461	1.197
delta_Rv3811	-0.32	1.389
delta_Rv0954	-0.605	1.797
PonA1	-0.433	-0.076
EccD1_KO	0.135	-0.487
EspI_KO	0.713	0.585
PE35_KO	0.12	1.467
PPE68_KO	0.32	1.181
glycerol2	-0.046	0.429
lignocerate	0.557	0.793
oleate	-0.437	-0.089
phosphatidylcholine	0.246	0.84
acetate	0.256	1.405
glucAc	0.797	1.081
Rv0950ko	-0.326	-1.263
Rv1096ko	-0.745	0.039
Rv3684ko	-1.896	-1.49
delta_otsA_trehalose	-1.174	0.441